1
|
Toh SI, Elaine Keisha J, Wang YL, Pan YC, Jhu YH, Hsiao PY, Liao WT, Chen PY, Ko TM, Chang CY. Discovery and characterization of genes conferring natural resistance to the antituberculosis antibiotic capreomycin. Commun Biol 2023; 6:1282. [PMID: 38114770 PMCID: PMC10730852 DOI: 10.1038/s42003-023-05681-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 12/06/2023] [Indexed: 12/21/2023] Open
Abstract
Metagenomic-based studies have predicted an extraordinary number of potential antibiotic-resistance genes (ARGs). These ARGs are hidden in various environmental bacteria and may become a latent crisis for antibiotic therapy via horizontal gene transfer. In this study, we focus on a resistance gene cph, which encodes a phosphotransferase (Cph) that confers resistance to the antituberculosis drug capreomycin (CMN). Sequence Similarity Network (SSN) analysis classified 353 Cph homologues into five major clusters, where the proteins in cluster I were found in a broad range of actinobacteria. We examine the function and antibiotics targeted by three putative resistance proteins in cluster I via biochemical and protein structural analysis. Our findings reveal that these three proteins in cluster I confer resistance to CMN, highlighting an important aspect of CMN resistance within this gene family. This study contributes towards understanding the sequence-structure-function relationships of the phosphorylation resistance genes that confer resistance to CMN.
Collapse
Affiliation(s)
- Shu-Ing Toh
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
| | - Johan Elaine Keisha
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
| | - Yung-Lin Wang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan, ROC
| | - Yi-Chi Pan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
| | - Yu-Heng Jhu
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
| | - Po-Yun Hsiao
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
| | - Wen-Ting Liao
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
| | - Po-Yuan Chen
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
| | - Tai-Ming Ko
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
| | - Chin-Yuan Chang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC.
- Center for Intelligent Drug Systems and Smart Bio-devices, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC.
- Department of Biomedical Science and Environment Biology, Kaohsiung Medical University, Hsinchu, 80708, Taiwan, ROC.
| |
Collapse
|
2
|
McLoughlin NM, Albers MA, Collado Camps E, Paulus J, Ran YA, Neubacher S, Hennig S, Brock R, Grossmann TN. Environment-Responsive Peptide Dimers Bind and Stabilize Double-Stranded RNA. Angew Chem Int Ed Engl 2023; 62:e202308028. [PMID: 37603459 DOI: 10.1002/anie.202308028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 08/23/2023]
Abstract
Double-stranded RNAs (dsRNA) possess immense potential for biomedical applications. However, their therapeutic utility is limited by low stability and poor cellular uptake. Different strategies have been explored to enhance the stability of dsRNA, including the incorporation of modified nucleotides, and the use of diverse carrier systems. Nevertheless, these have not resulted in a broadly applicable approach thereby preventing the wide-spread application of dsRNA for therapeutic purposes. Herein, we report the design of dimeric stapled peptides based on the RNA-binding protein TAV2b. These dimers are obtained via disulfide formation and mimic the natural TAV2b assembly. They bind and stabilize dsRNA in the presence of serum, protecting it from degradation. In addition, peptide binding also promotes cellular uptake of dsRNA. Importantly, peptide dimers monomerize under reducing conditions which results in a loss of RNA binding. These findings highlight the potential of peptide-based RNA binders for the stabilization and protection of dsRNA, representing an appealing strategy towards the environment-triggered release of RNA. This can broaden the applicability of dsRNA, such as short interfering RNAs (siRNA), for therapeutic applications.
Collapse
Affiliation(s)
- Niall M McLoughlin
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Marvin A Albers
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Estel Collado Camps
- Department of Medical BioSciences, Radboud University, Nijmegen Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Jannik Paulus
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Youri A Ran
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Saskia Neubacher
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Incircular B.V., De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Sven Hennig
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Roland Brock
- Department of Medical BioSciences, Radboud University, Nijmegen Medical Center, 6525 GA, Nijmegen, The Netherlands
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, 293, Bahrain
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| |
Collapse
|
3
|
Paternoga H, Crowe-McAuliffe C, Bock LV, Koller TO, Morici M, Beckert B, Myasnikov AG, Grubmüller H, Nováček J, Wilson DN. Structural conservation of antibiotic interaction with ribosomes. Nat Struct Mol Biol 2023; 30:1380-1392. [PMID: 37550453 PMCID: PMC10497419 DOI: 10.1038/s41594-023-01047-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/26/2023] [Indexed: 08/09/2023]
Abstract
The ribosome is a major target for clinically used antibiotics, but multidrug resistant pathogenic bacteria are making our current arsenal of antimicrobials obsolete. Here we present cryo-electron-microscopy structures of 17 distinct compounds from six different antibiotic classes bound to the bacterial ribosome at resolutions ranging from 1.6 to 2.2 Å. The improved resolution enables a precise description of antibiotic-ribosome interactions, encompassing solvent networks that mediate multiple additional interactions between the drugs and their target. Our results reveal a high structural conservation in the binding mode between antibiotics with the same scaffold, including ordered water molecules. Water molecules are visualized within the antibiotic binding sites that are preordered, become ordered in the presence of the drug and that are physically displaced on drug binding. Insight into RNA-ligand interactions will facilitate development of new antimicrobial agents, as well as other RNA-targeting therapies.
Collapse
Affiliation(s)
- Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | | | - Lars V Bock
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Timm O Koller
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Martino Morici
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Bertrand Beckert
- Dubochet Center for Imaging at EPFL-UNIL, Batiment Cubotron, Lausanne, Switzerland
| | | | - Helmut Grubmüller
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Jiří Nováček
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
| |
Collapse
|
4
|
Epinecidin-1, a marine antifungal peptide, inhibits Botrytis cinerea and delays gray mold in postharvest peaches. Food Chem 2023; 403:134419. [DOI: 10.1016/j.foodchem.2022.134419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/25/2022] [Accepted: 09/25/2022] [Indexed: 11/22/2022]
|
5
|
Three-dimensional structure-guided evolution of a ribosome with tethered subunits. Nat Chem Biol 2022; 18:990-998. [PMID: 35836020 PMCID: PMC9815830 DOI: 10.1038/s41589-022-01064-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/17/2022] [Indexed: 01/11/2023]
Abstract
RNA-based macromolecular machines, such as the ribosome, have functional parts reliant on structural interactions spanning sequence-distant regions. These features limit evolutionary exploration of mutant libraries and confound three-dimensional structure-guided design. To address these challenges, we describe Evolink (evolution and linkage), a method that enables high-throughput evolution of sequence-distant regions in large macromolecular machines, and library design guided by computational RNA modeling to enable exploration of structurally stable designs. Using Evolink, we evolved a tethered ribosome with a 58% increased activity in orthogonal protein translation and a 97% improvement in doubling times in SQ171 cells compared to a previously developed tethered ribosome, and reveal new permissible sequences in a pair of ribosomal helices with previously explored biological function. The Evolink approach may enable enhanced engineering of macromolecular machines for new and improved functions for synthetic biology.
Collapse
|
6
|
Evaluation of Susceptibility of the Human Pathogen Helicobacter pylori to the Antibiotic Capreomycin. ScientificWorldJournal 2022; 2022:8924023. [PMID: 35958801 PMCID: PMC9357814 DOI: 10.1155/2022/8924023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/23/2022] Open
Abstract
Helicobacter pylori infection causes gastritis, peptic ulcer disease, mucosa-associated lymphoid tissue lymphoma, and gastric cancer and can also promote thrombosis. It is estimated that approximately 4.5 billion individuals are infected, thus rendering H. pylori the most prevalent microbial pathogen. Currently established regimes for antibiotic treatment are massively challenged by increasing drug resistance and the development of novel antimicrobial therapies is urgently required. The antibiotic capreomycin is clinically used against multiple drug-resistant strains of Mycobacterium tuberculosis. It targets the complex between TlyA, a hemolysin- and RNA-binding protein, and the bacterial rRNA. In this study we have explored the possible antibacterial effects of capreomycin against several strains of H. pylori and found only moderate activity which was comparable to metronidazole-resistant strains. Molecular docking of capreomycin to TlyA proteins from H. pylori and M. tuberculosis identified several residues within TlyA which interact with the drug; however, binding affinities of H. pylori– TlyA for capreomycin appear to be higher than those of Mycobacterium– TlyA. The data suggest that capreomycin may warrant further investigations into its potential use as antibiotic against H. pylori.
Collapse
|
7
|
Laughlin ZT, Nandi S, Dey D, Zelinskaya N, Witek MA, Srinivas P, Nguyen HA, Kuiper EG, Comstock LR, Dunham CM, Conn GL. 50S subunit recognition and modification by the Mycobacterium tuberculosis ribosomal RNA methyltransferase TlyA. Proc Natl Acad Sci U S A 2022; 119:e2120352119. [PMID: 35357969 PMCID: PMC9168844 DOI: 10.1073/pnas.2120352119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/22/2022] [Indexed: 11/18/2022] Open
Abstract
Changes in bacterial ribosomal RNA (rRNA) methylation status can alter the activity of diverse groups of ribosome-targeting antibiotics. These modifications are typically incorporated by a single methyltransferase that acts on one nucleotide target and rRNA methylation directly prevents drug binding, thereby conferring drug resistance. Loss of intrinsic methylation can also result in antibiotic resistance. For example, Mycobacterium tuberculosis becomes sensitized to tuberactinomycin antibiotics, such as capreomycin and viomycin, due to the action of the intrinsic methyltransferase TlyA. TlyA is unique among antibiotic resistance-associated methyltransferases as it has dual 16S and 23S rRNA substrate specificity and can incorporate cytidine-2′-O-methylations within two structurally distinct contexts. Here, we report the structure of a mycobacterial 50S subunit-TlyA complex trapped in a postcatalytic state with a S-adenosyl-L-methionine analog using single-particle cryogenic electron microscopy. Together with complementary functional analyses, this structure reveals critical roles in 23S rRNA substrate recognition for conserved residues across an interaction surface that spans both TlyA domains. These interactions position the TlyA active site over the target nucleotide C2144, which is flipped from 23S Helix 69 in a process stabilized by stacking of TlyA residue Phe157 on the adjacent A2143. Base flipping may thus be a common strategy among rRNA methyltransferase enzymes, even in cases where the target site is accessible without such structural reorganization. Finally, functional studies with 30S subunit suggest that the same TlyA interaction surface is employed to recognize this second substrate, but with distinct dependencies on essential conserved residues.
Collapse
Affiliation(s)
- Zane T. Laughlin
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA 30322
| | - Suparno Nandi
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Natalia Zelinskaya
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Marta A. Witek
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Pooja Srinivas
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Graduate Program in Molecular and Systems Pharmacology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA 30322
| | - Ha An Nguyen
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Department of Chemistry Graduate Program, Emory University, Atlanta, GA 30322
| | - Emily G. Kuiper
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | | | - Christine M. Dunham
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Emory Antibiotic Resistance Center, Emory University, Atlanta, GA 30322
| | - Graeme L. Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Emory Antibiotic Resistance Center, Emory University, Atlanta, GA 30322
| |
Collapse
|
8
|
Jia H, Chu H, Dai G, Cao T, Sun Z. Rv1258c acts as a drug efflux pump and growth controlling factor in Mycobacterium tuberculosis. Tuberculosis (Edinb) 2022; 133:102172. [PMID: 35158297 DOI: 10.1016/j.tube.2022.102172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 01/17/2022] [Accepted: 01/23/2022] [Indexed: 11/27/2022]
Abstract
The possible role of efflux pump as a survival mechanism in Mycobacterium tuberculosis (M. tb) is gaining an increasing attention. Previously, Rv1258c (Tap) and its certain mutations confer the clinically relevant drug resistance. In this study, we found new mutations of Rv1258c in G195C, T297P and I328T. Effect of modulating T297P and I328T on the drug resistance by knockout and complement in M. tb H37Rv showed that M. tb ΔRv1258c showed a slightly lower MIC for rifampin, ethambutol, ofloxacin, amikacin, capreomycin and streptomycin than M. tb H37Rv WT and the complement. Rv1258c T297P and Rv1258c I328T showed an increased drug resistance to ethambutol and capreomycin than the complement of Rv1258c WT. Most importantly, M. tb ΔRv1258c exhibited a slow growth in the normal culture medium. TMT-based quantitative proteomics analysis of M. tb ΔRv1258c and WT showed that the knockout of Rv1258c greatly down-regulated the expression of the ribosome system and one of the special five type VII secretion systems, ESX-3, which impaired the bacterial growth. These results indicate that the newly found T297P and I328T mutations of Rv1258c contributed to an increased resistance to ethambutol and capreomycin, and Rv1258c as growth controlling factor influencing the growth of M. tb.
Collapse
Affiliation(s)
- Hongbing Jia
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China; Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Hongqian Chu
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China; Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Guangming Dai
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China; Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Tingming Cao
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China; Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Zhaogang Sun
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China; Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China.
| |
Collapse
|
9
|
Pan YC, Wang YL, Toh SI, Hsu NS, Lin KH, Xu Z, Huang SC, Wu TK, Li TL, Chang CY. Dual-Mechanism Confers Self-Resistance to the Antituberculosis Antibiotic Capreomycin. ACS Chem Biol 2022; 17:138-146. [PMID: 34994196 DOI: 10.1021/acschembio.1c00799] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Capreomycin (CMN) is an important second-line antituberculosis antibiotic isolated from Saccharothrix mutabilis subspecies capreolus. The gene cluster for CMN biosynthesis has been identified and sequenced, wherein the cph gene was annotated as a phosphotransferase likely engaging in self-resistance. Previous studies reported that Cph inactivates two CMNs, CMN IA and IIA, by phosphorylation. We, herein, report that (1) Escherichia coli harboring the cph gene becomes resistant to both CMN IIA and IIB, (2) phylogenetic analysis regroups Cph to a new clade in the phosphotransferase protein family, (3) Cph shares a three-dimensional structure akin to the aminoglycoside phosphotransferases with a high binding affinity (KD) to both CMN IIA and IIB at micromolar levels, and (4) Cph utilizes either ATP or GTP as a phosphate group donor transferring its γ-phosphate to the hydroxyl group of CMN IIA. Until now, Cph and Vph (viomycin phosphotransferase) are the only two known enzymes inactivating peptide-based antibiotics through phosphorylation. Our biochemical characterization and structural determination conclude that Cph confers the gene-carrying species resistance to CMN by means of either chemical modification or physical sequestration, a naturally manifested belt and braces strategy. These findings add a new chapter into the self-resistance of bioactive natural products, which is often overlooked while designing new bioactive molecules.
Collapse
Affiliation(s)
- Yi-Chi Pan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010 Taiwan, R.O.C
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 30010 Taiwan, R.O.C
| | - Yung-Lin Wang
- Genomics Research Center, Academia Sinica, Taipei, 11529 Taiwan, R.O.C
| | - Shu-Ing Toh
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010 Taiwan, R.O.C
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 30010 Taiwan, R.O.C
| | - Ning-Shian Hsu
- Genomics Research Center, Academia Sinica, Taipei, 11529 Taiwan, R.O.C
| | - Kuan-Hung Lin
- Genomics Research Center, Academia Sinica, Taipei, 11529 Taiwan, R.O.C
| | - Zhengren Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Sheng-Cih Huang
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, 30010 Taiwan, R.O.C
| | - Tung-Kung Wu
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010 Taiwan, R.O.C
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 30010 Taiwan, R.O.C
| | - Tsung-Lin Li
- Genomics Research Center, Academia Sinica, Taipei, 11529 Taiwan, R.O.C
| | - Chin-Yuan Chang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010 Taiwan, R.O.C
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 30010 Taiwan, R.O.C
- Center for Intelligent Drug Systems and Smart Bio-devices, National Yang Ming Chiao Tung University, Hsinchu, 30010 Taiwan, R.O.C
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, 80708 Taiwan, R.O.C
| |
Collapse
|
10
|
Laughlin ZT, Conn GL. Tuberactinomycin antibiotics: Biosynthesis, anti-mycobacterial action, and mechanisms of resistance. Front Microbiol 2022; 13:961921. [PMID: 36033858 PMCID: PMC9403184 DOI: 10.3389/fmicb.2022.961921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 07/21/2022] [Indexed: 12/04/2022] Open
Abstract
The tuberactinomycins are a family of cyclic peptide ribosome-targeting antibiotics with a long history of use as essential second-line treatments for drug-resistant tuberculosis. Beginning with the identification of viomycin in the early 1950s, this mini-review briefly describes tuberactinomycin structures and biosynthesis, as well as their past and present application in the treatment of tuberculosis caused by infection with Mycobacterium tuberculosis. More recent studies are also discussed that have revealed details of tuberactinomycin action on the ribosome as well as resistance mechanisms that have emerged since their introduction into the clinic. Finally, future applications of these drugs are considered in the context of their recent removal from the World Health Organization's List of Essential Medicines.
Collapse
Affiliation(s)
- Zane T Laughlin
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States.,Graduate Program in Biochemistry, Cell and Developmental Biology (BCDB), Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, United States
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States.,Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, GA, United States
| |
Collapse
|
11
|
Belardinelli R, Sharma H, Peske F, Rodnina MV. Perturbation of ribosomal subunit dynamics by inhibitors of tRNA translocation. RNA (NEW YORK, N.Y.) 2021; 27:981-990. [PMID: 34117118 PMCID: PMC8370747 DOI: 10.1261/rna.078758.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/03/2021] [Indexed: 05/02/2023]
Abstract
Many antibiotics that bind to the ribosome inhibit translation by blocking the movement of tRNAs and mRNA or interfering with ribosome dynamics, which impairs the formation of essential translocation intermediates. Here we show how translocation inhibitors viomycin (Vio), neomycin (Neo), paromomycin (Par), kanamycin (Kan), spectinomycin (Spc), hygromycin B (HygB), and streptomycin (Str, an antibiotic that does not inhibit tRNA movement), affect principal motions of the small ribosomal subunits (SSU) during EF-G-promoted translocation. Using ensemble kinetics, we studied the SSU body domain rotation and SSU head domain swiveling in real time. We show that although antibiotics binding to the ribosome can favor a particular ribosome conformation in the absence of EF-G, their kinetic effect on the EF-G-induced transition to the rotated/swiveled state of the SSU is moderate. The antibiotics mostly inhibit backward movements of the SSU body and/or the head domains. Vio, Spc, and high concentrations of Neo completely inhibit the backward movements of the SSU body and head domain. Kan, Par, HygB, and low concentrations of Neo slow down both movements, but their sequence and coordination are retained. Finally, Str has very little effect on the backward rotation of the SSU body domain, but retards the SSU head movement. The data underscore the importance of ribosome dynamics for tRNA-mRNA translocation and provide new insights into the mechanism of antibiotic action.
Collapse
Affiliation(s)
- Riccardo Belardinelli
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Heena Sharma
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| |
Collapse
|
12
|
Parajuli NP, Mandava CS, Pavlov MY, Sanyal S. Mechanistic insights into translation inhibition by aminoglycoside antibiotic arbekacin. Nucleic Acids Res 2021; 49:6880-6892. [PMID: 34125898 PMCID: PMC8266624 DOI: 10.1093/nar/gkab495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/17/2021] [Accepted: 05/26/2021] [Indexed: 11/13/2022] Open
Abstract
How aminoglycoside antibiotics limit bacterial growth and viability is not clearly understood. Here we employ fast kinetics to reveal the molecular mechanism of action of a clinically used, new-generation, semisynthetic aminoglycoside Arbekacin (ABK), which is designed to avoid enzyme-mediated deactivation common to other aminoglycosides. Our results portray complete picture of ABK inhibition of bacterial translation with precise quantitative characterizations. We find that ABK inhibits different steps of translation in nanomolar to micromolar concentrations by imparting pleotropic effects. ABK binding stalls elongating ribosomes to a state, which is unfavorable for EF-G binding. This prolongs individual translocation step from ∼50 ms to at least 2 s; the mean time of translocation increases inversely with EF-G concentration. ABK also inhibits translation termination by obstructing RF1/RF2 binding to the ribosome. Furthermore, ABK decreases accuracy of mRNA decoding (UUC vs. CUC) by ∼80 000 fold, causing aberrant protein production. Importantly, translocation and termination events cannot be completely stopped even with high ABK concentration. Extrapolating our kinetic model of ABK action, we postulate that aminoglycosides impose bacteriostatic effect mainly by inhibiting translocation, while they become bactericidal in combination with decoding errors.
Collapse
Affiliation(s)
- Narayan Prasad Parajuli
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124 Uppsala, Sweden
| | - Chandra Sekhar Mandava
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124 Uppsala, Sweden
| | - Michael Y Pavlov
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124 Uppsala, Sweden
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124 Uppsala, Sweden
| |
Collapse
|
13
|
Hsu SH, Zhang S, Huang SC, Wu TK, Xu Z, Chang CY. Characterization of Enzymes Catalyzing the Formation of the Nonproteinogenic Amino Acid l-Dap in Capreomycin Biosynthesis. Biochemistry 2020; 60:77-84. [PMID: 33356147 DOI: 10.1021/acs.biochem.0c00808] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Capreomycin (CMN) and viomycin (VIO) are nonribosomal peptide antituberculosis antibiotics, the structures of which contain four nonproteinogenic amino acids, including l-2,3-diaminopropionic acid (l-Dap), β-ureidodehydroalanine, l-capreomycidine, and β-lysine. Previous bioinformatics analysis suggested that CmnB/VioB and CmnK/VioK participate in the formation of l-Dap; however, the real substrates of these enzymes are yet to be confirmed. We herein show that starting from O-phospho-l-Ser (OPS) and l-Glu precursors, CmnB catalyzes the condensation reaction to generate a metabolite intermediate N-(1-amino-1-carboxyl-2-ethyl)glutamic acid (ACEGA), which undergoes NAD+-dependent oxidative hydrolysis by CmnK to generate l-Dap. Furthermore, the binding site of ACEGA and the catalytic mechanism of CmnK were elucidated with the assistance of three crystal structures, including those of apo-CmnK, the NAD+-CmnK complex, and CmnK in an alternative conformation. The CmnK-ACEGA docking model revealed that the glutamate α-hydrogen points toward the nicotinamide moiety. It provides evidence that the reaction is dependent on hydride transfer to form an imine intermediate, which is subsequently hydrolyzed by a water molecule to produce l-Dap. These findings modify the original proposed pathway and provide insights into l-Dap formation in the biosynthesis of other related natural products.
Collapse
Affiliation(s)
- Sheng-Hsin Hsu
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30010, Taiwan, ROC
| | - Shouqi Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Sheng-Cih Huang
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu 30010, Taiwan, ROC
| | - Tung-Kung Wu
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30010, Taiwan, ROC
| | - Zhengren Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Chin-Yuan Chang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30010, Taiwan, ROC.,Center for Intelligent Drug Systems and Smart Bio-devices, National Chiao Tung University, Hsinchu 30010, Taiwan, ROC
| |
Collapse
|